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23  structures 8670  species 0  interactions 16728  sequences 126  architectures

Family: TatD_DNase (PF01026)

Summary: TatD related DNase

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

The Pfam group coordinates the annotation of Pfam families in Wikipedia, but we have not yet assigned a Wikipedia article to this family. If you think that a particular Wikipedia article provides good annotation, please let us know.

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

TatD related DNase Provide feedback

This family of proteins are related to a large superfamily of metalloenzymes [1]. TatD, a member of this family has been shown experimentally to be a DNase enzyme.

Literature references

  1. Holm L, Sander C; , Proteins 1997;28:72-82.: An evolutionary treasure: unification of a broad set of amidohydrolases related to urease. PUBMED:9144792 EPMC:9144792

  2. Wexler M, Sargent F, Jack RL, Stanley NR, Bogsch EG, Robinson C, Berks BC, Palmer T; , J Biol Chem 2000;275:16717-16722.: TatD is a cytoplasmic protein with DNase activity. No requirement for TatD family proteins in sec-independent protein export. PUBMED:10747959 EPMC:10747959


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR001130

This entry represents the TatD family, which includes TatD and many putative deoxyribonucleases and metal-dependent hydrolases. The family is related to a large superfamily of metalloenzymes [ PUBMED:9144792 ]. TatD has been shown to be a 3'-5' exonuclease that processes single-stranded DNA in DNA repair [ PUBMED:10747959 , PUBMED:25114049 ].

In E. coli TatD is encoded by a operon that encodes Tat proteins, including TatA, TatB, and TatC, for protein transport via the Tat (Twin-Arginine Translocation) pathway. However, TatD is not involved in the protein export in the Tat pathway [ PUBMED:10747959 ].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Amidohydrolase (CL0034), which has the following description:

This family includes a large family of metal dependent amidohydrolase enzymes [1].

The clan contains the following 17 members:

A_deaminase Amidohydro_1 Amidohydro_2 Amidohydro_3 AMP_deaminase CpsB_CapC DHOase DUF3604 DUF6282 Peptidase_M19 PHP PHP_C PTE RNase_P_p30 TatD_DNase Urease_alpha UxaC

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB sequence database. More...

View options

We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(79)
Full
(16728)
Representative proteomes UniProt
(74640)
RP15
(2712)
RP35
(8160)
RP55
(16116)
RP75
(27068)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(79)
Full
(16728)
Representative proteomes UniProt
(74640)
RP15
(2712)
RP35
(8160)
RP55
(16116)
RP75
(27068)
Alignment:
Format:
Order:
Sequence:
Gaps:
Download/view:

Download options

We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(79)
Full
(16728)
Representative proteomes UniProt
(74640)
RP15
(2712)
RP35
(8160)
RP55
(16116)
RP75
(27068)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1370 (release 3.0)
Previous IDs: UPF0006;
Type: Domain
Sequence Ontology: SO:0000417
Author: Bateman A
Number in seed: 79
Number in full: 16728
Average length of the domain: 254.60 aa
Average identity of full alignment: 26 %
Average coverage of the sequence by the domain: 88.48 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 20.5 20.5
Trusted cut-off 20.5 20.5
Noise cut-off 20.4 20.4
Model length: 255
Family (HMM) version: 23
Download: download the raw HMM for this family

Species distribution

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Selections

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This visualisation provides a simple graphical representation of the distribution of this family across species. You can find the original interactive tree in the adjacent tab. More...

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Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the TatD_DNase domain has been found. There are 23 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0R0I6Y9 View 3D Structure Click here
A0A1D6E240 View 3D Structure Click here
A0A1D6ERR2 View 3D Structure Click here
A0A1D6F9F8 View 3D Structure Click here
A0A1D6IGY3 View 3D Structure Click here
A0A1D6IGY3 View 3D Structure Click here
A0A1D6J4H6 View 3D Structure Click here
A0A1D6JCS3 View 3D Structure Click here
A0A1D6JMJ5 View 3D Structure Click here
A0A1D6P822 View 3D Structure Click here
A0A1D6PKS6 View 3D Structure Click here
A0A1D8PS00 View 3D Structure Click here
A0A2R8Q8H0 View 3D Structure Click here
A2RVM4 View 3D Structure Click here
A4HRW3 View 3D Structure Click here
A4HV34 View 3D Structure Click here
A4I2Q1 View 3D Structure Click here
A4ICZ0 View 3D Structure Click here
B7ZNL9 View 3D Structure Click here
C6TNW0 View 3D Structure Click here
D3ZT26 View 3D Structure Click here
F1M484 View 3D Structure Click here
F1QWD1 View 3D Structure Click here
F1QY16 View 3D Structure Click here
F4J6X3 View 3D Structure Click here
G5EG18 View 3D Structure Click here
I1MNS0 View 3D Structure Click here
K7K6V1 View 3D Structure Click here
K7MHG6 View 3D Structure Click here
M0R5U3 View 3D Structure Click here
M0R6T1 View 3D Structure Click here
O08343 View 3D Structure Click here
P0AFQ7 View 3D Structure Click here
P27859 View 3D Structure Click here
P34220 View 3D Structure Click here
P38430 View 3D Structure Click here
P39408 View 3D Structure Click here
P41890 View 3D Structure Click here
P90989 View 3D Structure Click here
Q0D8I5 View 3D Structure Click here
Q17R31 View 3D Structure Click here
Q2G1S2 View 3D Structure Click here
Q3U1C6 View 3D Structure Click here
Q4CRN2 View 3D Structure Click here
Q4D723 View 3D Structure Click here
Q4DFW5 View 3D Structure Click here
Q4DQC9 View 3D Structure Click here
Q4DUR0 View 3D Structure Click here
Q503T5 View 3D Structure Click here
Q54KD6 View 3D Structure Click here
Q54N91 View 3D Structure Click here
Q54SD3 View 3D Structure Click here
Q54YD3 View 3D Structure Click here
Q55DK1 View 3D Structure Click here
Q58171 View 3D Structure Click here
Q58527 View 3D Structure Click here
Q58778 View 3D Structure Click here
Q58977 View 3D Structure Click here
Q5ADU7 View 3D Structure Click here
Q6GML7 View 3D Structure Click here
Q6P1N9 View 3D Structure Click here
Q6P8M1 View 3D Structure Click here
Q6Z130 View 3D Structure Click here
Q7JUN9 View 3D Structure Click here
Q7XUG9 View 3D Structure Click here
Q8I226 View 3D Structure Click here
Q93075 View 3D Structure Click here
Q9SRQ4 View 3D Structure Click here
Q9U2N7 View 3D Structure Click here
Q9U2Q7 View 3D Structure Click here
Q9UUF1 View 3D Structure Click here
Q9VDC1 View 3D Structure Click here